Hi Rissi. You are on medication that will have a very good impact on reducing these microbes, however, there are immunologic factors to consider.
What lead you to this treatment? Did you have absolute confirmation about intestinal protozoa?
My experience has been that this is a multifaceted problem, often with blood cell\tissue involvement.
The protozoa in the gut are mostly nuisance parasites which alter gut microbiota, and cause itchy bum. In more sever cases, there is acute digestive upset which can last for years.
Can you write down all your symptoms? Take your time, because details are very important in these cases.
Do you have any past blood work etc. that you can get access to? Shroom